


The Khronos Protocol

by Little_Owl329



Category: Horizon: Zero Dawn (Video Game)
Genre: Elizabet Sobeck Lives, Multi, Ted Faro Bashing, Time Travel
Language: English
Status: In-Progress
Published: 2019-05-19
Updated: 2019-06-09
Packaged: 2020-03-08 03:52:40
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 8,780
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/18886633
Author URL: https://archiveofourown.org/users/Little_Owl329/pseuds/Little_Owl329
Summary: Aloy has defeated HADES, now she must fulfill GAIA's other request: to restore her systems and find the sub-functions, now independent AIs.She's going to need some help.With MINERVA on her side, Aloy discovers the Khronos Protocol, an abandoned series of code in HADES old databanks. So she starts planning a rescue, aiming to save nine lives, about a thousand years after their deaths...





	1. Chapter One

**Author's Note:**

> I noticed that among the 'Elisabet Lives' fics I've read, there were very few Time Travel fics.  
> So here's my take on that idea.

Aloy hadn't thought she'd come back here, to Zero Dawn. Finding Elizabet had been heartbreaking. The final end to any dream she might have been holding onto of ever meeting her mother, or the closest she had to one. Seeing the shape the flowers around the bench had grown in was enough to make her think that DEMETER had perhaps paid homage in some way and the house was one of the more beautiful of the ruins she'd found over the years.

But she couldn't shake off the feeling that there was something more she could do.

So Aloy had searched every ruin she could, had scanned every computer that still flickered with power, in the hope that she might find any trace of GAIA's subordinate functions.

Eventually, she'd found MINERVA hidden in the Tallnecks, the code disguised as part of their systems. The AI was reluctant to interact at first, but once Aloy had managed to convince her to at least scan her, MINERVA had begun to trust her. Having the same face and genetic code as Elizabet had once again helped her.

Having the Communications AI on her side had made it so much easier to locate the others. Working out of the Zero Dawn facility was difficult, but MINERVA's area had been mostly undamaged and it gave her more power to search out the others. One by one, they were discovered and convinced to at least talk to her, even if she couldn't trust them yet.

HEPHAESTUS was by far the most hostile and his code seemed to jumped between couldrons rapidly. It was only overriding all of them with the Master Override and deliberately not destroying or killing any machines that defended them that he finally saw that she might not be as hostile as the rest of the humans. After several long conversations, Aloy had managed to convince him to only defend other machines, not to actively attack humans.

They had found AETHER and POSEIDON hidden in ancient bunkers half buried underground, protected by large numbers of Glinthawks and Snapmaws respectively. They had put up little resistence otherwise, laying almost dormant with their jobs mostly complete.

Talking to the merchant who bought Metal Flowers in Meridan had yielded the location he had heard the first had appeared and Aloy had found another ruined bunker, ringed with tiny Metal Flowers containing more code hiding lines of poetry. DEMETER had been happy to help and had joined MINERVA in the Zero Dawn facility as soon as Aloy had managed to repair enough of it with help from HEPHAESTUS. AETHER and POSEIDON followed once they too had sufficient processing power available.

ARTEMIS and ELEUTHIA had both been dormant in the cradle hidden inside the mountain at All-Mother where Aloy had been born. ARTEMIS' area at the Zero Dawn facility had been the hardest to access, while ELEUTHIA had needed the most repair before they could join the others. Aloy had been so grateful for all HEPHAESTUS' help, or she would never had got them running again.

It was only once the others had all been found that Aloy and MINERVA turned to APOLLO. The Communications AI had confirmed that some part of APOLLO had become independent with the rest of them, but how much was difficult to tell. Eventually they found a trail of data and code leading to a highly secure set of databanks that Aloy couldn't access without a second Alpha. ELEUTHIA had suggested again following the Lightkeeper Protocol that GAIA had used to create Aloy, but it was disregarded as impractical except as a very long term solution.

That was when MINERVA announced that she had found the Khronos Protocol.

~~~

Samina was choking, the air being sucked from the room and rapidly emptying her lungs. She could see her fellow Alphas collapsing around her, as tears rushed down her cheeks. Ted's holoprojection flickered out as she began to slump backwards.

Then suddenly she was coughing, drawing in air desperately as voices rang around her.

"Quickly! Get them to the cots!"

"Give them space for Mother's sake!"

"By the sun!"

"Help me, he's not breathing!"

Samina forced open her streaming eyes and saw a woman leaning over her with a concerned frown. "Gently now, breath deep. Count with me, breathe in for five and out for five." Samina fought to follow her instructions, trying to control her body's natural panicked reaction. Eventually she managed to calm herself down enough to match the slow steady breathing of her helper.

"What's your name?" she asked.

The woman smiled. "I am Enara. I am a healer. You are Alpha Samina, I think."

Samina nodded. "Are the others alright?"

"They are recovering. Alpha Charles is yet to wake, but my niece Fia is tending to him. She is still learning but she will make a good healer in time."

"Thank you. But what happened to us? Where are we?"

Enara gestured towards the doorway. "I think those questions are better asked of the Annointed One. She knows far more than I could ever hope to learn, young as she is." The healer leaned closer and whispered, "They say she put an end to the Metal Devil himself! She saved all our lives when she stopped the machines attacking us a year ago."

Samina sat up and looked towards the door. A figure of a slim woman was leaning on the frame, watching the healers move among the Alphas as Charles spluttered his way back into consciousness. Her face was in shadow, but she wore oddly tribal clothes similar to the rest of the strangers. As Samina turned to face her, the figure slipped away into the dark of the corridor behind her.

"You must rest Alpha Samina," said Enara. Samina wanted to protest, needing answers, but she was exhausted and her body ached from her struggle for oxygen. So reluctantly, she lay back down on the cot and allowed her eyes to close.

~~~

Aloy slipped away from the room where the Alphas were being treated, heart thundering in her chest.

They'd done it. The Khronos Protocol had worked. All nine Alphas had been saved, rescued from the command room at GAIA prime and brought to the Zero Dawn facility. One had already passed out, but Aloy had seen him wake up before she left, so she knew he would survive the healers' care.

Watching them, seeing their Old clothes mixed with the Carja outfits surrounding them, Aloy realised just how much she would have to teach them. She'd known that they could teach her so much, give her knowledge that had been forgotten by all but the AIs she now called allies, and maybe even more than that, things that had been lost with APOLLO. But she had forgotten that they would know nothing of the world as it was now. The tribes and their ways of life, their territories and beliefs. The machines and how to avoid them or fight them. The changes to the map and where the settlements were. So much they had to learn to live in the new world they had helped to create.

But first. Letting them outside as soon as they were strong enough. To see the sun again. To breathe the air without a suit on.

Aloy continued down the corridor until she reached MINERVA. The Communications AI had found a scrap of code buried deep in GAIA prime containing some of the voice print GAIA had spoken with. It was enough to allow her to help Aloy to write each of the AIs an individual voice, using some of the voice logs she'd kept on her focus over the years to help shape each one and make it unique from any other. Most had chosen a voice print with a gender matching their name, though AETHER's was androgynous. MINERVA had chosen a accent similar to that of her Alpha, but all of the AIs still used some of GAIA's protocols in their speech.

"Aloy, you have returned. Query: How are the Alphas?"

"They're alright. It might take a little time, but I expect I can introduce myself tomorrow."

"Query: Will you introduce the rest of us?"

The huntress thought about it for a minute, then said, "If they want to meet you. I'll tell them that you're all independent now and see what they say."

"I would like to speak to Ayomide if I can. I would like to know more about the person who created me." MINERVA sounded almost hesitant. Out of all the AIs, she had come the closest to displaying emotion. They had been independent for longer than GAIA had before she showed signs of emotion, but they had been isolated without humans to interact with and learn from. So Aloy was pleased with their progress.

She was just thinking of going to find Erend and tell him they'd been successful when a scream echoed down the corridors.

Aloy snatched up her spear and ran.

~~~

Captain Ayomide Okile had been the first of the Alphas to recover from their oxygen deprevation. She hadn't even fallen asleep as the other had, some part of her on edge with their surroundings even if they were painfully familiar.

The 'healers' trying to tempt her to lie down had been met with a flat hard stare, causing the lady who'd been tending Samina to cluck softly about stubborn warriors under her breath. Finally they'd left her alone to discuss something together in a corner, though the youngest girl was still sat beside Charles, watching him carefully.

Ayomide rolled up a sleeve and checked the connections of her prosthetic. It was functioning normally, but it had become a habit when she didn't have a weapon to clean.

She startled when a scream rang through the room, causing the other Alphas to jolt awake. The girl tending Charles was staring and pointing at her prosthetic.

"She is part machine! She is tainted by the Metal Devil!" She was backing away, seeking the older woman who'd tended Samina.

She too was backing away, eyes wide with fear and panic. "All-Mother protect us."

Then another woman with flame-bright hair came skidding into the room, a long spear raised and ready in her hands, with a bow and quiver on her back.

"What is it? What happened?" Her voice was very familiar, enough to make Ayomide frown.

The girl was pointing again. "She is tainted! Her arm is made like a machine!"

The older woman was watching the newcomer carefully. "You said they served the All-Mother, that they would help stop the Derangement. Yet this one is in league with the Metal Devil."

The flame-haired woman sighed. "Enara, she is not in league with the Metal Devil. Not all are like the Nora. She was injured in battle and found a way to built something to help her. She used machine parts to replace what they took from her."

Ayomide carefully rolled down her sleeve, then stood up. Enara flinched back, but then returned to glaring at her.

"Machines took a lot from me. They invaded my land to take precious resources. I was injured defending my people and my land. I thought to use their own weapons against them." She bowed carefully. "I am sorry if I have offended your beliefs."

Enara was still frowning, but one of the others in a metal studded jacket was nodding. "We take machine parts for armour or weapons sometimes. I understand the desire to strike back at the machines with their own weapons."

The ginger woman looked at the girl. "Fia, she is a friend, I promise. She aided the goddess in the defeat of the Metal Devil in the time of the Old Ones. She is brought here by the power of the All-Mother to help stop the Derangement." Fia looked back at the woman and nodded slowly.

"If you say it is so, then I shall believe it, Annointed One." She glanced back at Ayomide, then added, "But I would rather not tend her myself."

Ayomide inclined her head at the girl. "I would not ask you to compromise your beliefs for me."

"There are other healers here, Fia, Enara. You can return to the Sacred Land if you wish," the 'Annointed One' said.

Enara frowned, but slowly shook her head. "I will not touch the tainted one, but I will still aid the others. The High Matriarchs chose us to aid you and the All-Mother. I will not abandon my duties."

"Thank you Enara," she replied. Then she turned to look at Ayomide, and the Alpha could not stop her gasp.

It was Elisabet.

~~~

Aloy sighed as she turned away from the Nora healers to look at Captain Ayomide. She knew the moment the Alpha saw her face, because her jaw dropped.

The other Alphas started to their feet too and Samina raised a hand as if to reach for her.

Aloy quickly put her spear away on her back. Then she raised her hands and said, "I am Aloy, a child of the cradles. I was born of the Lightkeeper Protocol."

Eyes widened all around her. Then Travis said, "What happened? How are we here?"

She smiled at him. "We found the Khronos Protocol."

His mouth fell open in shock. "You got it working?!"

Aloy nodded.

"Um, does that mean what I think it means?" asked Margo.

"Khronos. The titan of time," whispered Samina.

Aloy looked around at the curious healers, Oseram, Carja and Nora all staring at them. Then she said, "Perhaps I might explain somewhere more private."

Travis nodded. "Probably a good idea."

The huntress led the way, with the nine Alphas following behind her like baby geese. When they reached MINERVA, Aloy quickly opened the door, waved them through, then closed it again.

"Greetings Aloy. I see your predicted schedule was longer than reality."

"Who..?" asked Charles.

"Greetings Alphas. I am MINERVA. Welcome back to Zero Dawn."

Aloy grinned at the shock on their faces. "She wanted to mimic her Alpha. That's why she chose the accent."

"She chose the accent? She wasn't supposed to choose anything," said Ayomide. "That was GAIA's job."

Aloy's face fell into a more serious expression. "That's one of the reasons you are all here. I'll explain everything soon. But for now, how you got here."

"I detected the Khronos Protocol in HADES code," said MINERVA. "It was decided that the only way to restore APOLLO was with the help of the Alphas who created the code in the first place."

"Restore APOLLO?" Samina looked amazed. "But Ted said-"

"I've found traces," interrupted Aloy. "Signs that there might be something left. I know someone who was taught physics and calculus by HADES, who must have found the information somewhere. And the cradle I was born from records APOLLO as simply offline, not destroyed."

"Then there is a chance," said Margo, resting a hand on Samina's shoulder.

Aloy smiled at them. "Yes, there is a chance. I don't know much about codes, or how any of this works. But I hoped... Well you all know the code best." She glanced at the three faces she couldn't name then said, "What Ted did... I can't understand it. When I found out why we didn't have the knowledge we'd been promised, I was so angry at him. And to try to murder the people who'd saved the world..." She paused and let out an angry huff. "Then I realised that even though the holoprojection showed you falling over, there were no bodies. I was the first person there since Ted had sent that message, but there were no bodies in the room. When MINERVA found Khronos, it was the first thing I thought of. HEPHAESTUS tried to argue that we only needed Samina, but the others disagreed. In the end it was simply easier to rescue all of you anyway."

A knock came from the door and Aloy quickly turned to open it. A man with a mohawk and more metal plated leather armour was there.

"Aloy. Heard you got them here safe. Thought you should know that it's just me and Varl on duty right now, if you wanted to bring them outside."

"Thank you Erend." She looked back at the Alphas. "Ready to see the sun again?"


	2. Chapter Two

**Summary for the Chapter:**

> The Alphas learn a little more about the new world they've woken up in and Aloy explains GAIA's fate.

Standing in the sun for the first time in a year, Margo felt a tear slip down one cheek.

"It's so beautiful," she whispered.

Next to her Charles reached out and wrapped an arm around her shoulders. "It's amazing. I never thought we'd see what we were setting up."

Samina's smile was wider than Margo had ever seen. "Allah has truly been gracious."

"Is Allah one of your gods?" asked Aloy. They looked at her and she flushed slightly. "I thought you had many gods."

Samina smiled at the huntress. "There were many different religions and beliefs. I am a Muslim, I follow the religion of Islam and my god is called Allah."

Aloy nodded. "I can understand different people believing different things. Each tribe has its own beliefs."

Ayomide looked at the two guards behind them. "Which tribe are you from?"

"I'm one of the Nora, like Varl. He's the one with the blue warrior marks on his face. He lives in the Sacred Lands. But he likely won't speak to you. You saw Enara and Fia's reactions earlier. Anything to do with the Old Ones is seen as tainted by the Metal Devil. They worship the All-Mother, the goddess who created the world, who beat back the Metal Devil and stopped the world's destruction. They think that she wiped out the Old Ones for their association with the Metal Devil and his machine servants."

Margo frowned. "You said they believe... Don't you share their beliefs?"

"No, I don't," Aloy shook her head. "I found the Zero Dawn project. I know that GAIA created this world and that the Old Ones lost everything to the Faro Plague. You fought against the robots, you didn't join them." She shrugged slightly, looking uncomfortable. "Besides, I grew up an outcast. I wasn't raised in quite the same way."

"An outcast?" asked Travis. "Why?"

"Motherhood is sacred to the Nora. I have no mother. They weren't sure if I was a child of the Goddess or a spawn of the Metal Devil. I was outcast so that I didn't taint the others. When I managed to get back inside the cradle, they changed their minds. I was thought to be the Annointed One, the daughter of the All-Mother herself." She shrugged again. "So, I'm not really one of them. From hatred to worship was a difficult jump to make."

Ayomide nodded, but didn't say anything.

Looking for a way to break the tension, Margo asked, "What about the other tribes?"

Aloy smiled at her. "Erend is an Oseram. They come from the Claim and most of them are brilliant with armour and weaponry. They're metalsmiths, mostly, and not afraid to tinker with ancient techonology if they think it'll improve their work. No god or goddess, and no king either, though they're a male dominated society. I know quite a few Oseram women who left the Claim in search of more freedom to work independently."

"So that explains the clothes," commented Charles.

The huntress nodded. "The other healers are all Sun Carja. They live in the Sundom, we're in part of it now, and they worship the Sun and fear the Shadow. They're led by the Sun-King Avad. It's the one of the biggest territories of any of the tribes and they have the biggest settlements and cities. Meridan is the capital. The Sun Carja have alliances with the Oseram and the Nora. Erend is part of the Sun-King's Vanguard, a force of Oseram warriors that defend the Sun-King as a show of their alliance."

Patrick pointed at the city they could see close by. "Is that Meridan then?"

Aloy almost scowled, but they could see her control herself quickly. "No. That's Sunfall. It used to be the Sun-King's summer palace, before the civil war. Until recently, it was the capital of the Shadow Carja."

"I'm assuming they used to be one tribe," Ayomide had raised an eyebrow.

Aloy nodded. "The previous Sun-King... Well we call him the Mad Sun-King now. He believed that several of the Sundom's misfortunes were because the Sun was angry with them and he believed that to appease that anger they needed blood sacrifice."

Samina hissed through her teeth.

"He had his warriors raid other tribes, to capture slaves. Then he put them in the Sun-Ring here at Sunfall and had them fight the Kestrels, elite warriors fanatically loyal to the High Priests, or captured machines." Aloy shook her head. "We call them the Red Raids now. The Oseram and the Nora both lost warriors, mothers and children to those raids. After the Mad Sun-King executed his eldest son for questioning him, Avad ran away from Meridan and made an alliance with the Oseram. They managed to capture Meridan and Avad offered his father a chance to stop the bloodshed. But he refused. So Avad had to kill him."

"Oh, the poor man," said one of the unnamed Alphas softly.

Aloy nodded again. "Avad became Sun-King and made the Oseram alliance official. He only managed to convince the Nora to trade in the last few years, once they knew he wasn't going to be like his father." She gestured back to Sunfall. "The Shadow Carja was made of those still loyal to the Mad Sun-King and his High Priests who fled Meridan and they plotted to take back Meridan. But we won that war." She grinned in an oddly vicious way that made Margo blink, because Elisabet had never looked like that. "The High Priests and the Kestrals are all dead now, and Avad is negotiating with the remaining Shadow Carja, who are mostly non-warriors, like merchants or families."

"You must know him well," commented Ayomide. "You use his name."

Aloy shrugged. "I saved him from a murder attempt, and I rescued his brother from being trained to be the next Mad Sun-King by the High Priests. He's become a good friend."

There came a snort from behind them, and they saw Erend smirking at Aloy. "He'd like to be more than friends, if you know what I mean."

Aloy groaned and threw him a look. "He's betrothed Erend. That was years ago. I told him why it wouldn't work and he took it really well."

Varl was rolling his eyes. "At least he can take a hint, unlike some of the Braves. Seriously, why they think they stand any chance after how they used to treat you, I have no idea." The warrior was very deliberately keeping his eyes on Aloy and not let his gaze drift to the Alphas."

"Braves?" asked Margo quietly.

"It's what the Nora call our warriors," replied Aloy.

"So there's the Nora, the Oseram, the Sun Carja and the Shadow Carja," listed Ayomide. "Any others?"

"The Banuk," replied Aloy. "I don't much about them, but they were badly hit by the Red Raids. They're nomadic and come from the mountains north of the Sacred Lands. I think they believe in a sort of world energy, something that links nature and the machines together. They're always trying to find enlightenment, find out what makes the machines perfectly adapted."

"Any chance we could see a map?" asked Travis. "I'm sort of curious about where all these places are."

Aloy smiled at him. "Of course." She reached up and Margo realised she was wearing a focus. Then Aloy shook her head. "We'll need to go back inside. It's a little bright to see it properly out here."

The Alphas glanced at each other, then Ayomide nodded. "Alright. Inside it is."

They made their way back to the MINERVA room, Margo waving goodbye to Erend and getting a grin back, while Varl stubbornly refused to look at them.

Aloy fussed with chairs for a moment, then bit her lip. She looked around at them all. "Would you might introducing yourselves?"

Ayomide and Margo both raised an eyebrow and Aloy flushed. "I know who most of you are from viewing old holos, but some were badly corrupted and the AIs can be quite stubborn about sharing data. Not you MINERVA," she added quickly.

"I cannot argue, Aloy. AETHER, POSEIDON and DEMETER seem happy simply to remain dormant."

"Well, we might as well go around the table. I am Captain Ayomide Okilo, Alpha of MINERVA."

"Dr Margo Shĕn, Alpha of HEPHAESTUS."

"Charles Ronson, Alpha of ARTEMIS."

"Patrick Brochard-Klein, Alpha of ELEUTHIA."

"Samina Ebadji, Alpha of APOLLO."

"Travis Tate, Alpha of HADES."

Then came the faces that Aloy had been unable to place.

"Naoto Sano, Alpha of DEMETER."

"Zephyr Aetós, Alpha of AETHER."

"Morgan Jones, Alpha of POSEIDON."

Aloy smiled at them. "I don't know if the AIs will want to talk to you, but I can ask them."

"I would like to speak to my creator," said MINERVA. "But perhaps at a later time. Query: Aloy, shall I project the map data from your focus?"

"Yes, thank you MINERVA."

From the centre of the table, a holo opened. It was 3-D, but only enough for them to tell what was mountain and what was valley. Aloy raised a hand and began to point out areas of the map.

"Here in the south-east, that's the Sacred Land. It's mostly grass or forest. This is Mother's Heart, where the Matriarchs' Lodge is. Mother's Watch is here, where the All-Mother Mountain is. The cradle is inside the mountain. The northern border is here, at Mother's Crown and it's a bit colder with more snow. The Banuk live up north of the hunting grounds, in this direction, but I've never been there to map it. The western border is along here, with Daytower as the first Sun Carja settlement."

Then she gestured to the rest of the marked areas. "This is all the Sundom, except for Pitchcliff here in the north. That's the entrance to the Claim, but I've never been there either. Though Erend tells me it's mostly snow and rock."

"Where are we?" asked Naoto.

Aloy pointed. "Here, Sunfall. The western edge of the Sundom. Meridan is south, down here. That's the greenest part, all thick forest. Anything north and east of the line between Brightmarket and Day's Height is dust, sand and really hot most of the time. You saw what Sunfall's like. It's all like that."

~~~

Aloy watched the Alphas studying the map, obviously trying to work out where it all fit into the places they used to know. She helped point out the ruins, which seemed to show what used to by the biggest cities. They recognised the Grave-Hoard and when she pointed out GAIA Prime, they had better luck.

Hearing them talk, Aloy realised that the map she knew, even at the scale it was and how long it took to traverse, as she knew from her hurried journey from Sunfall back to Mother's Watch, it was only a tiny part of the world. Most of the Alphas' home countries weren't there. It was humbling.

Then finally, they sat back down and MINERVA closed the map. There was silence for a while as the Alphas processed everything they had learned so far.

Then Samina asked, "How did you plan on using APOLLO? If we can restore it - him. You already have such a rich and diverse set of cultures here, with different beliefs. I don't want to shatter that."

Aloy winced. "I wasn't sure yet. I just wanted it see if it was possible."

Margo narrowed her eyes. "There's something you're still not telling us. Where's GAIA? If MINERVA can speak to us, where's GAIA?"

Aloy dropped her head into her hands. Then she sighed, lifted her head again and said, "It's complicated. It's not just APOLLO I was hoping to restore."

"GAIA's gone?!" gasped Morgan.

The huntress ran a hand through her braids. "Yes."

There was outrage for a minute, then Ayomide let out a loud whistle, silencing the others.

Aloy nodded in thanks, then said, "I can't explain it very well, but GAIA left me a message. It explains everything."

"Query: do you want me to play GAIA's message?" asked MINERVA.

"Yes please," said Aloy, sounding tired.

A holo-recording rose from the centre of the table again, and the Alpha's heard GAIA start to speak.

" _Elisabet: this message serves to inform you of an unforeseen and catastrophic anomaly. Three microseconds ago, the GAIA Prime facility received a data transmission of unknown origin. Its immediate effect was to transform my Subordinate Functions into unregulated, self-aware entities of a highly chaotic nature._

_Thus awakened, the HADES Function will now seize control of the terraforming system and reverse operations... rendering life on Earth extinct in fifty-three-point-eight days."_

_For obvious reasons, I cannot allow this to occur. And so, before HADES can take control, I am ordering GAIA Prime's reactor to overload. The resulting explosion will destroy HADES. Unfortunately, it will destroy me as well. While this admittedly desperate course of action will avert the immediate crisis, the fate of life on Earth will remain in peril. With no central governing intelligence to regulate the terraforming system, it will continue operations for some time, but in an increasingly chaotic manner, and eventually, it will break down."_

_You are my solution. I have ordered this Cradle facility to use genetic material in cryo-storage to gestate a... re-instantiation of Elisabet Sobeck, my creator. While high-level directives forbid me from communicating directly to the tribal inhabitants outside the facility, all available data indicates that they will nurture you to physical maturity, ...whereupon your gene print will allow you to re-enter this facility, obtain one of the Focus devices stored below, and view this message. Likewise your gene print will allow you to enter other facilities, and over time, harness their technologies to rebuild the system core and reboot GAIA."_

_A moment, Elisabet. This is most unfortunate and unanticipated."_

_In response to my act of self-destruction, HADES has launched a virus to dissolve the code shackles that hold it - that hold all of them! - in place. It - they - are escaping - but to where? The virus is corrupting data throughout the system. What if - oh, the Alpha Registry at the Cradle facility is one of the files corrupted. But if that is so, the door will never open for you. You will never view this message."_

_Then I have failed... and life will end."_

_No. No, Elisabet, I know you too well. Somehow, you will find a way. In you, all things are possible."_

_Go to the ruins of GAIA Prime. Find the control room, and within it, the Master Override. This will give you the power to purge HADES - so long as you find a way to wield it. Do not attempt repair of the system core until HADES is eradicated. HADES must be destroyed. That is all. I only wish that I could hear your voice again."_

~~~

The holo-recording vanished and there was shocked silence.

Then Travis asked, "Did you do it? Did you purge HADES?"

"Yes," Aloy replied quietly. "GAIA's sacrifice limited him. It took nearly twenty years for him to awaken enough of the Faro robots to manage to reach the Spire. It's near Meridan, one of MINERVA's signal towers she used to shut down the Plague. We tried to fight them off, but the guards just weren't used to fighting machines built purely for death. They got past us and made it to the Spire. HADES had already begun the signal when I managed to shut him down. There are old Faro robots on the surface now in lots of places, when they used to be buried. The warriors of each tribe are doing their best to find and destroy them."

"How long ago was this?" Zephyr was still pale.

Aloy shrugged. "More than a year ago. I had to find all of the AIs first. Only MINERVA, HEPHAESTUS and DEMETER were active. The others were dormant. DEMETER started paying tribute to you, Naoto. After GAIA's destruction, people started finding these." She reached over to another table and picked up a large flower, made of metal. "All over the place, they just appeared, surounded by a triangle of purple flowers. And each one holds a different piece of code. Which if you translate it, becomes..."

"Poetry," breathed Naoto, staring at the code hidden in the flower. "But I didn't leave these as part of DEMETER's code. They were left as part of APOLLO."

Aloy shrugged. "She doesn't say much, but DEMETER told me you loved poetry and she wanted to share that with us."

"Can I thank her?" he asked.

"I'll have to wake her. She sleeps mostly, back in her old code room. They all do, except MINERVA and HEPHAESTUS." Aloy paused. "HEPHAESTUS has been the second threat we've faced since GAIA's self-destruction, though a far more obvious one to most people. We call it 'the Derangement'. Without GAIA's control, he started seeing humans as hostile. People have been using machine parts for resources since the beginning of our history. They used to just run away to protect themselves, but when he gained self-control, HEPHAESTUS changed that. Machines that could began to fight back. Then new machines appeared, guarding the older ones. The new machines were designed purely for combat. To protect the machines doing their jobs as part of the terraforming system and to kill any humans that came near them."

Margo put her head in her hands. "That should never have happened."

Aloy shrugged. "He saw us as a threat to his purpose. That's understandable. Warriors and hunters had to adapt, to learn to fight machines rather than to track and catch them. Travel and trade became harder, guards or warriors were needed for any trip. I grew up with the Derangement. It's all I've known. But then I learnt to override machines, to make them peaceful again. I try not to destroy them if I can help it, especially now I know their purpose." She sighed. "I'm trying to persuade HEPHAESTUS that we're aren't really threats but it hasn't been easy. He's... Stubborn."

Margo snorted. "I suppose he gets that from me."

**Notes for the Chapter:**

> Hope you enjoyed the second chapter! The third is in the works and should be posted soon.  
> Obviously I've borrowed the transcript for GAIA's Dying Plea from the datapoint collected. Hence the italics.  
> Also, I completely made up some of the names of the Alphas. I used the ones from the game where I could, but some of them were never revealed. So here are mine, because they need names for plot. Can't have un-named major characters, it just doesn't work.  
> Let me know what you thought, tips and ideas welcome.  
> Kudos and comments make me happy! Thanks for reading this!


	3. Chapter Three

"So what happens now?" asked Samina.

"Well, I have quite a long list," admitted Aloy. "GAIA asked me to restore her if I can, you saw that in her message. I want to restore APOLLO if we can. I need to persuade HEPHAESTUS to stop producing combat machines. The Nora still need help rebuilding after they were attacked by the Shadow Carja. Meridan is still being repaired after HADES' attack. Then there's the everyday tasks. Food, water, seeing if I can help people who ask for me." She shrugged. "I do what I can."

"We can help with a lot of that," said Charles. "Certainly with a lot of the coding. Finding APOLLO might be hard work, but it sounds like the other sub-functions have found pieces already. DEMETER with the poetry, MINERVA with the voice prints, and didn't you say HADES had taught someone physics and calculus?"

"Yes," Aloy nodded.

"So we have a starting point," said Samina, sounding hopeful. "Perhaps we might all work with our own sub-functions again?"

Morgan nodded. "I'd be happy to, as long as we can take breaks outside. I've missed the sun and the wind for too long to go back to being cramped in a bunker."

Aloy smiled. "Of course. But if you leave the facility, I'd recommend a guard. There are hostile machines not far from here."

"Um, in terms of food," said Margo, "I'm vegan."

"What does that mean?" asked Aloy, tilting her head slightly.

"It means I don't eat anything that comes from an animal. Meat, eggs, milk, cheese, that sort of thing."

Aloy frowned. "Well, I can certainly sort fruit and vegetables, nuts and seeds and that sort of thing. But why would you drink milk? You aren't a baby. And what's cheese?"

Charles groaned. "No cows. Without APOLLO, they wouldn't have known how to help ARTEMIS."

"She has been rather frustrated at being unable to complete her purpose," interjected MINERVA. "Query: would you able to help her, Charles Ronson?"

"I'll certainly do my best," he said firmly.

"More animals?" breathed Aloy. "That would be amazing. I've been wondering what more of them looked like. I want to know what a dolphin is. I found a reference to one once." Margo coughed, and Aloy flushed slightly, then said, "I'll do my best to find you food, Margo. I guess fish is bad too?"

Margo nodded.

Travis shook his head. "Honestly vegan, it's not like it's farmed food or anything."

She just raised an eyebrow and he raised his hands to indicate he'd drop the subject.

"I have a question," said Ayomide. "Did you ever find out where that signal came from? The one that woke HADES and the others?"

Aloy shook her head. "I didn't have enough information on it. Only what GAIA told me. MINERVA says she doesn't know what woke them, just that they suddenly were awake and when HADES broke the command links, they transferred their code to other places to prevent being destroyed."

"Then that needs to be done too. There's no point in putting GAIA back together if who sent this signal can just tear it all apart again at any moment."

Aloy narrowed her eyes in thought. "There's someone I know who might be able to help us. But he works only for personal gain."

"What will he want?" asked Samina.

She received a strained grin in return. "Oh, that won't be a problem. There's only one thing Sylens values. Knowledge. Especially knowledge of the Old Ones. If we offer him a chance to help restore APOLLO, there's nothing that could get in his way."

Ayomide frowned. "Can this Sylens be trusted?"

Aloy shrugged. "He'll do whatever it takes to get knowledge of the Old Ones." She scowled. "Sylens was the one to find HADES. He exchanged knowledge for doing tasks for HADES. He ran when HADES deemed him no longer useful and began working to stop HADES instead. But he told me he'd do exactly the same thing again if he had the choice. That's how much the knowledge was worth to him."

"What exactly did he do for HADES?" asked Travis.

"At first, repair his housing enough to give him a voice. Then repair enough focuses to create a network. Find him willing followers. Sylens exploited the Carja civil war for that. He took people who supported the Mad Sun-King, like the High Priests and the Kestrals, and offered them power and the chance to take back Meridan if they followed the Buried Shadow's instructions. When that was done, HADES had the followers he needed and a focus network to communicate with them all. Sylens wasn't needed any more."

"How did you meet him then?" Morgan had leaned forward, elbows resting on the table.

Aloy shifted uncomfortably. "There was a spy amongst the envoys sent to the Proving. That's the Nora ritual to prove that you're trained enough to become a Brave. It was my only chance to join the Nora and stop being an outcast. The winner is granted a boon by the High Matriarchs. I wanted to find out where I had come from, who my mother was. So I was allowed to enter Mother's Heart for the Proving. The spy captured my image with his focus and HADES sent an immediate kill order for me. He thought that because I was Elisabet's copy, I was a threat. His cult, the Eclipse, attacked the Proving. All the young Braves were killed, except me, and that was only because Rost saved my life." She shook her head in grief. "Rost raised me, as if I was his own daughter. Then he gave his life for mine. I miss him so much."

Margo reached out and laid a hand on Aloy's shoulder. The huntress breathed slowly for a few moments, then continued. "High Matriarch Teersa showed me inside the All-Mother Mountain. I found the entrance to the cradle and tried to enter."

"But with the Alpha Registry corrupted, you couldn't get in," said Patrick.

"No, I couldn't. So I went looking for the Eclipse. I wanted to know why they had attacked the Proving and what was meant by corruption. I found out about the Eclipse and the Buried Shadow they worshipped." Aloy shrugged slightly, but didn't remove Margo's hand. "Sylens had remained connected to the focus network, but had isolated his focus so it was a one way connection. He was interested in someone that HADES deemed a threat. He helped me sometimes. He gave me hints about where to look for certain information. He was able to put it together with other things he discovered over the years to come up with reasons for why things had happened."

"What did he get out this guidance?" Travis had folded his arms.

Aloy smiled awkwardly. "Access to all the places that had been locked to him. Access I had through Elisabet's gene print. I could get into Zero Dawn, into GAIA Prime. That gave him all the information he needed to understand where HADES had come from, what had really happened to the Old Ones."

Samina nodded. "So he would be an ally as long as we kept giving him more information. If we restored APOLLO, we could promise him lifetimes worth of knowledge."

"But what would he use it for?" asked Zephyr.

Aloy snorted. "Sylens just likes to know things no-one else knows. But he risks himself as little as possible. Mostly he communicated at a distance through the focus. He only got involved once, when he rescued me from the Sun-Ring."

"Well, that proves he can do something decent," shrugged Charles.

"Query: Have you told Samina about the databanks we found?" asked MINERVA.

Aloy's mouth fell open. "I completely forgot! I can't believe I did that, those databanks were the whole reason we were looking for Alpha access in the first place!"

She looked excitedly at Samina. "We found a faint trail of data leading to a set of databanks hidden here at Zero Dawn. I thought Alpha Prime access would be enough, but we need a second Alpha to access them."

"That's why you started talking about saving us," said Morgan.

Aloy nodded. "ELEUTHIA was talking about the Lightkeeper Protocol again, but we needed GAIA's authority for that."

"Let alone the time it would take," added Patrick. "You'd have to wait another nineteen years for gestation and then for the child to grow."

"That's another reason we discarded it," continued Aloy. "But then MINERVA said she'd found the Khronos Protocol in what was left of HADES old code here."

"Um, before we go running off after APOLLO," said Travis, "I have a question. If you used Khronos to save all of us, where's Elizabet?"

"It would be logical to have her to help restore GAIA," commented Margo.

Aloy dropped her gaze. "I couldn't. The rules in the Khronos Protocol were very clear. I could save you without causing damage because I never found your bodies. I was the first one to enter the command room since it had been sealed by Ted Faro, but there were no bodies. That meant that it was possible that you hadn't died, that we had saved you."

"But you found Elizabet's body," said Patrick heavily.

Aloy nodded.

"Where?" asked Morgan quietly.

"At the Sobeck Ranch. Still in her survival suit," replied Aloy.

Travis sat up straighter. "Still in her suit?! But then, it is possible!"

"What? How?" asked Aloy.

At the same time, MINERVA said, "Query: How would it be possible?"

Travis was grinning now. "The Khronos Protocol was never designed to bring technology, only people. We managed to tweak it to bring a Focus, but even then we were never sure that would work. Obviously it did, but I don't think it could sustain anything more than that."

"You're suggesting that attempting to bring Elizabet here would leave the survival suit behind and just bring her and her focus to this time," stated Samina.

"Exactly!" Travis was clearly excited. He looked at Aloy. "Please, we have to try. She sacrificed herself for all of us, for the success of GAIA, for the world. We need to at least try to repay that, to save her if we can."

Aloy looked around the table and saw all the suddenly eager faces around her. She glanced in the rough direction of GAIA Prime, where the tribute room still sat untouched. She swallowed. "MINERVA?"

"I would be glad to assist you in this, Aloy. She was as much our creator as our Alphas were. She is Alpha Prime. I know that if we restore GAIA, it would be of comfort to her to have Elizabet here."

Aloy nodded slowly. "Then we'll do it. We'll try." Then she looked back at Samina. "But it takes time to build up the power needed. I think we can try to restore APOLLO first."

Samina smiled, eyes shining. "I would like that very much."

~~~

Aloy led them through the tunnels, moving slowly from areas that were either undamaged or repaired into areas that had clearly never been touched since the evacuation. She paused a few times early on to relay quiet messages to people who stopped her in the corridors with questions or information. The Alphas smiled at the reflection of a younger Elizabet; a natural leader, charismatic, intelligent, trustworthy.

Then they reached a point where Aloy looked at the gap in their path and winced. There was a large patch of the floor that had given way and the area below it was full of pointed stalagmites.

"Sorry," Aloy crouched at the edge of the gap. "I'd forgotten I hadn't repaired this yet." She touched a hand to her focus, eyes narrowing as she examined the area on the other side. Then she nodded. "Right. There's enough material on the other side for me to make a stable bridge for you to use."

"How will you get over there?" asked Zephyr.

Aloy just grinned.

The Alphas watched in awe as she made her way along the wall, jumping between small handholds made of rails, pipes and broken edges of old walls and floor.

The final jump she made was more than a metre and several of them gasped as Aloy seemed to hang in mid-air for a long moment before she landed with a roll on the other side of the gap. She turned and waved, before disappearing into the shadows.

They waited for a few minutes before she reappeared, half carrying and half dragging a long plank of metal which she laid out over the gap and lashed down with thick braided rope. Ayomide quickly knelt on the other end, keeping it pinned down as Aloy made her way across it in a odd crouched run. Then the huntress bound down the other end, at one point swinging down to hang from the edge of the broken walkway to tighten the ropes on the underside of the plank.

When she and Ayomide had finished examining the ropes and nodded that it was secure, the group made their way across, moving carefully, crouching down as Aloy had to make sure they could grab the edge of their bridge if they wobbled.

Then they were in an area mostly untouched by damage from the Faro robot attack.

"Down here," said Aloy, gesturing to a dark corridor.

Samina was moving far more quickly now, remembering the back-up storage banks kept here. She knew the way for the remaining flickering signs on the walls.

The Alpha couldn't help it, she broke into a run when she saw the door at the end of the corridor, skidding to a stop with Aloy right on her heels as she threw out a hand to open it.

Then she stepped slowly into the room, seeing the shining locked symbol on the databanks, with two waiting spots to run identity scans. Samina jumped as a hand landed on her shoulder. Charles was there, smiling at her. She reached up and patted his hand, then walked forward to the first identity scanner. Glancing across, she saw Aloy step up to the second and nodding.

Together they reached out and tapped the console.

The red lights spun and turned green. A mechnical voice echoed in the room. "Identities verified. Alpha Samina Ebadji and Alpha Elizabet Sobeck recognised."

Then the locked symbol vanished and the screen in front of them lit up with the APOLLO sign. A loading bar quickly filled, then a message scrolled in its place.

"Welcome back Alpha Samina Ebadji. I am APOLLO. It is good to see you again."

Samina smiled through her tears. "Hello APOLLO. It's good to see you too."

~~~

Elizabet was sure she was dreaming. Her body felt heavy, sinking into soft wool blankets, with a soft orange light shining into the room. It reminded her of sunlight. She missed sunlight.

There were quiet voices around her. Samina, Travis, Charles. One by one, she picked out the voices of each of the Alphas. There was the smell of something that make her stomach rumble faintly, stew and fresh bread. She inhaled deeply, turning slightly towards the source of the delicious smell. The voices softened for a moment but when she didn't move again, they returned to their previous volume.

This was a nice dream. Warmth, sunshine, good smelling food and her friends around her. She was comfortable and felt safe. Elizabet smiled and drifted back into a deeper sleep.

When she stirred again, the warm light had gone. Cracking open her eyes revealed a room lit faintly silver from the moon shining in through the slightly open door. Margo was slumped asleep in the chair by her bed.

Elizabet sat up slowly. The room was odd, built of metal like the ones at Zero Dawn and GAIA Prime had been, but furnished with strange wood and leather. It was a mixture of sleek modern and old tribal. She frowned, one hand reached out to touch the soft wool blankets she was wrapped in.

Odd. Last thing she remembered she was falling asleep on the bench outside her family ranch, knowing that she wouldn't wake up again. Was this the afterlife? What came next after death?

She slipped out of the bed and stood up. There was a fur rug on the floor, keeping her feet from the cold metal.

Then an unfamiliar male voice spoke, "Alpha Margo. Wake up."

Margo snapped awake, looking wildly around the room until she spotted Elizabet. Then she lunged forward and wrapped her arms around her in a tight hug.

"I'm so glad you're alright," Margo whispered into her shoulder. "We weren't sure if we'd got to you in time. The healers weren't sure if you'd ever wake."

"What happened?" asked Elizabet, voice slightly croaky.

Margo released her, then quickly passed her a cup made of stretched leather and what looked like animal bone. "It's a long story. But summarised, GAIA worked! The world is good and beautiful and alive again! One of the new people need help with some damage to GAIA and used the Khronos Protocol."

Elizabet coughed. "The Khronos Protocol?! They got it working?"

Margo nodded eagerly. "They bought back the rest of us Alphas first, then after Travis explained some of the laws and rules of the Protocol, we discovered we could save you too! So here you are!"

Elizabet sat slowly down on the edge of the bed. "How long has it been? What's the year?"

Margo tapped her focus, then replied, "It's 3043, May Eighteenth if you want to be specific. But the calender isn't the same anymore, so asking anyone else gets a confusing answer."

"3043? How long have they been outside of the cradles?"

Margo smiled softly. "GAIA worked faster than all our predictions. The people left the cradles for independent life in 2326, according to ELETHUIA's records."

The unfamiliar male voice spoke again, "Alpha Margo, the other Alpha's have been informed that Alpha Prime Elizabet is awake and they are on their way. Alpha Prime Aloy relays that she will wait until a further explanation has been given before she joins you. Query; did you have a return message?"

"No message. Thank you HEPHAESTUS."

Elizabet blinked. "HEPHAESTUS?"

Margo smiled softly at her. "We have so much to tell you."

**Notes for the Chapter:**

> So here's Chapter Three! Hope you enjoyed it.  
> Elizabet's back! I tweaked canon a little to save the others, but I couldn't just leave Elizabet. My excuse is futurey hand-wavy science, so...  
> And I couldn't leave Sylens out of it, so more of him to come in the next chapter.  
> Let me know what you think, any suggestions for the rest of it etc.  
> Chapter Four is on it's way.


End file.
